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dev:major: covalent bond
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@YaoYinYing
YaoYinYing committed Aug 23, 2024
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155 changes: 155 additions & 0 deletions apps/protein_folding/helixfold3/data/7s69_glycan.sdf
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OpenBabel03042416223D

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$$$$
19 changes: 19 additions & 0 deletions apps/protein_folding/helixfold3/data/demo_7s69_coval.json
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{
"entities": [
{
"type": "protein",
"sequence": "DRHHHHHHKLGKMKIVEEPNSFGLNNPFLSQTNKLQPRVQPSPVSGPSHLFRLAGKCFNLVESTYKYELCPFHNVTQHEQTFRWNAYSGILGIWQEWDIENNTFSGMWMREGDSCGNKNRQTKVLLVCGKANKLSSVSEPSTCLYSLTFETPLVCHPHSLLVYPTLSEGLQEKWNEAEQALYDELITEQGHGKILKEIFREAGYLKTTKPDGEGKETQDKPKEFDSLEKCNKGYTELTSEIQRLKKMLNEHGISYVTNGTSRSEGQPAEVNTTFARGEDKVHLRGDTGIRDGQ",
"count": 1
},
{
"type": "ligand",
"sdf": "/repo/PaddleHelix/apps/protein_folding/helixfold3/data/7s69_glycan.sdf",
"count": 1
},
{
"type": "bond",
"bond": "A,ASN,74,ND2,B,UNK1,1,C,covale,2.3",
"_comment": "'A,74,ND2:B,1:CW,null' from RF2AA"
}
]
}
121 changes: 111 additions & 10 deletions apps/protein_folding/helixfold3/helixfold/data/pipeline_conf_bonds.py
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"""Functions for building the input features (reference ccd features) for the HelixFold model."""

import collections
from dataclasses import dataclass
import gzip
import os
import pickle
from typing import Any, Optional
import re
from typing import Any, List, Literal, Optional, Tuple

from absl import logging
from immutabledict import immutabledict
from helixfold.common import residue_constants
import numpy as np
from openbabel import openbabel

from helixfold.common import residue_constants
from helixfold.data.tools import utils



ALLOWED_LIGAND_BONDS_TYPE = {
"SING": 1,
"DOUB": 2,
Expand All @@ -22,6 +26,98 @@
"AROM": 12,
}

# Define the possible bond types as a Literal
BondType = Literal["covale", "metal", "hydrogen", "ionic", "disulfide", "aromatic"]


@dataclass
class AtomPartner:
"""
Represents one partner atom in a covalent bond.
Attributes:
label_asym_id (str): The asymmetry identifier for the partner atom (i.e., chain ID).
label_comp_id (str): The component identifier for the partner atom (i.e., residue name).
seq_id (str): The sequence identifier for the partner atom (merged label_seq_id and auth_seq_id).
label_atom_id (str): The atom identifier for the partner atom (i.e., atom name).
"""

label_asym_id: str # Chain ID
label_comp_id: str # Residue name
seq_id: str # Merged sequence ID
label_atom_id: str # Atom name


@dataclass
class CovalentBond:
"""
Represents a covalent bond between two atoms in a molecular structure.
Attributes:
atom_1 (AtomPartner): The first partner atom in the bond.
atom_2 (AtomPartner): The second partner atom in the bond.
bond_type (BondType): The type of the bond.
pdbx_dist_value (float): The distance value as defined in the PDBx/mmCIF format.
"""

atom_1: AtomPartner
atom_2: AtomPartner
bond_type: BondType
pdbx_dist_value: float

def parse_covalent_bond_input(input_string: str) -> List[CovalentBond]:
"""
Parses a human-readable string into a list of CovalentBond objects.
Args:
input_string (str): A string representing covalent bonds, where each bond is
described by two atom partners separated by a comma,
and multiple bonds are separated by semicolons.
Example: "A,GLY,25,CA,A,GLY,25,N,covale,1.32; B,HIS,58,ND1,B,HIS,58,CE1,covale,1.39"
Returns:
List[CovalentBond]: A list of CovalentBond objects.
"""
covalent_bonds = []

# Split the input string by semicolons to separate individual covalent bonds
bond_strings = input_string.split(';')

for bond_str in bond_strings:
# Split the individual bond string by commas to separate attributes
bond_parts = bond_str.split(',')

if len(bond_parts) != 10:
raise ValueError(f"Invalid bond format: {bond_str}. Expected 10 fields per bond.")

# Create AtomPartner instances for the two atoms in the bond
atom_1 = AtomPartner(
label_asym_id=bond_parts[0].strip(),
label_comp_id=bond_parts[1].strip(),
seq_id=bond_parts[2].strip(),
label_atom_id=bond_parts[3].strip()
)

atom_2 = AtomPartner(
label_asym_id=bond_parts[4].strip(),
label_comp_id=bond_parts[5].strip(),
seq_id=bond_parts[6].strip(),
label_atom_id=bond_parts[7].strip()
)

# Create a CovalentBond instance
covalent_bond = CovalentBond(
atom_1=atom_1,
atom_2=atom_2,
bond_type=bond_parts[8].strip(),
pdbx_dist_value=float(bond_parts[9].strip())
)

# Append the CovalentBond instance to the list
covalent_bonds.append(covalent_bond)

return covalent_bonds

def load_ccd_dict(ccd_preprocessed_path: str) -> immutabledict[str, Any]:
if not os.path.exists(ccd_preprocessed_path):
raise FileNotFoundError(f'[CCD] ccd_preprocessed_path: {ccd_preprocessed_path} not exist.')
Expand Down Expand Up @@ -151,7 +247,7 @@ def make_ccd_conf_features(all_chain_info, ccd_preprocessed_dict,
return features


def make_bond_features(covalent_bond, all_chain_info, ccd_preprocessed_dict,
def make_bond_features(covalent_bond: List[CovalentBond], all_chain_info, ccd_preprocessed_dict,
extra_feats: Optional[dict]=None):
"""
all_chain_info: dict, (chain_type_chain_id): ccd_seq (list of ccd), such as: protein_A: ['ALA', 'MET', 'GLY']
Expand All @@ -172,24 +268,29 @@ def make_bond_features(covalent_bond, all_chain_info, ccd_preprocessed_dict,
_set_chain_id_list = set(chain_id_list)
parsed_covalent_bond = []
for _bond in covalent_bond:
left_bond_atomid, right_bond_atomid = _bond['ptnr1_label_atom_id'], _bond['ptnr2_label_atom_id']
left_bond_name, right_bond_name = _bond['ptnr1_label_comp_id'], _bond['ptnr2_label_comp_id']
left_bond, right_bond = _bond['ptnr1_label_asym_id'], _bond['ptnr2_label_asym_id']
# Accessing the AtomPartner attributes for both atoms in the covalent bond
left_bond_atomid, right_bond_atomid = _bond.atom_1.label_atom_id, _bond.atom_2.label_atom_id
left_bond_name, right_bond_name = _bond.atom_1.label_comp_id, _bond.atom_2.label_comp_id
left_bond, right_bond = _bond.atom_1.label_asym_id, _bond.atom_2.label_asym_id

left_bond_idx, right_bond_idx = _bond['ptnr1_label_seq_id'], _bond['ptnr2_label_seq_id']
auth_left_idx, auth_right_idx = _bond['ptnr1_auth_seq_id'], _bond['ptnr2_auth_seq_id']
left_bond_idx, right_bond_idx = _bond.atom_1.seq_id, _bond.atom_2.seq_id
auth_left_idx, auth_right_idx = _bond.atom_1.seq_id, _bond.atom_2.seq_id

left_bond_idx = 1 if left_bond_idx == '.' else left_bond_idx
right_bond_idx = 1 if right_bond_idx == '.' else right_bond_idx

if _bond['bond_type'] != "covale":
if _bond.bond_type != "covale":
logging.warning(f'Ignore non-covale bond type: {_bond.bond_type}')
continue

if _bond['pdbx_dist_value'] > 2.4:
if _bond.pdbx_dist_value > 2.4:
# the covalent_bond is cut off by distance=2.4
logging.warning(f'Ignore bonding with distance > 2.4: {_bond.pdbx_dist_value}')
continue

## When some chainID is filtered, bond need to be filtered too.
if (left_bond not in _set_chain_id_list) or (right_bond not in _set_chain_id_list):
logging.warning(f'Ignore bonding with left and right out of chain list: ')
continue

parsed_covalent_bond.append([left_bond, left_bond_name, left_bond_idx, left_bond_atomid, auth_left_idx,
Expand Down
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